• # smfsb

• Referenced in 6 articles [sw12260]
• package smfsb: SMfSB 2e: Stochastic Modelling for Systems Biology, second edition. This package contains code ... data for modelling and simulation of stochastic kinetic biochemical network models. It contains the code ... second edition of the book Stochastic Modelling for Systems Biology, published by Chapman & Hall/CRC Press...
• # SABRE

• Referenced in 7 articles [sw12884]
• reaction networks. The importance of stochasticity within biological systems has been shown repeatedly during ... raised the need for efficient stochastic tools. We present SABRE, a tool for stochastic analysis ... reaction networks. Biochemical reactions networks represent biological systems studied at a molecular level and these ... time Markov chains. Besides operating in a stochastic mode, SABRE may also perform a deterministic...
• # STEPS

• Referenced in 18 articles [sw17866]
• STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python. We describe ... platform for modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional...
• # S-ROCK

• Referenced in 42 articles [sw11792]
• standard explicit methods proposed so far for stochastic problems and give significant speed improvement ... ROCK methods allows one to handle large systems without linear algebra problems usually encountered with...
• # ProbReach

• Referenced in 3 articles [sw20157]
• ProbReach: verified probabilistic delta-reachability for stochastic hybrid systems. We present ProbReach, a tool ... verifying probabilistic reachability for stochastic hybrid systems, i.e., computing the probability that the system reaches ... reachability that is suited for hybrid systems whose stochastic behaviour is given in terms ... several benchmarks involving highly non-linear hybrid systems...
• # AMYTISS

• Referenced in 2 articles [sw36936]
• automated controller synthesis for large-scale stochastic systems. In this paper, we propose a software ... controllers for large-scale discrete-time stochastic systems. This tool is employed to (i) build ... HWAs). Unlike all existing tools for stochastic systems, AMYTISS can utilize high-performance computing ... always present in analyzing large-scale stochastic systems. We benchmark AMYTISS against the most recent...
• # StochSens

• Referenced in 3 articles [sw13067]
• package, that implements sensitivity analysis for stochastic chemical systems using the concept of the Fisher ... Information Matrix for the stochastic systems without the need for Monte Carlo simulations...
• # iNA

• Referenced in 4 articles [sw17973]
• exploration of stochastic biochemical kinetics using the system size expansion. The accepted stochastic descriptions ... Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter ... analysis of stochastic biochemical kinetics by means of van Kampen’s system size expansion ... using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates...
• # prob-black-reach

• Referenced in 2 articles [sw34625]
• systems to be fully deterministic. For stochastic systems, statistical techniques are available. However, they cannot ... black-box checking technique for stochastic systems that allows both, non-deterministic and probabilistic behaviour...
• # SMART_

• Referenced in 33 articles [sw04097]
• Logical and stochastic modeling with smart. We describe the main features of Smart, a software ... logic and probabilistic analysis of complex systems. Smart can combine different formalisms in the same ... algorithms, are available. For the study of stochastic and timing behavior, both sparse-storage...

• Referenced in 5 articles [sw10690]
• system resulting in more compact models. In this paper, we enrich the stochastic process algebra ... presented in papers on the stochastic simulation of biological systems with delays. This semantics ... PEPAd systems in generalized semi-Markov processes (GSMPs), as input for a delay stochastic simulation ... deterministic framework for modeling of biological systems with delays. Finally, we prove theorems stating...
• # SpiCO

• Referenced in 10 articles [sw10691]
• stochastic pi calculus for concurrent objects. We present SpiCO, a new modeling ... simulation language for systems biology. SpiCO is based on the stochastic $pi$ calculus. It supports...
• # HSIM

• Referenced in 2 articles [sw18272]
• HSIM: A hybrid stochastic simulation system for systems biology. This paper describes a method ... best of two well known simulation approaches: Stochastic simulation of chemical ... reactions and Entity-centered (multi-agents) systems. The stochastic simulation algorithm and its enhanced versions...
• # Dsamala

• Referenced in 2 articles [sw15240]
• analysing and simulating discrete, continuous, stochastic dynamic systems. This article describes DSamala toolbox, a computational ... simulating and analysing discrete, continuous, stochastic dynamic systems; It is presented as a MATLAB toolbox...